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2021 journal cell chemical biology reimagining dots and dashes visualizing structure and function of organelles for high content imaging analysis marcus y chin jether amos espinosa grace pohan michelle r arkin sarine markossian doi https doi org 10 1002 cpz1 75 date march 18 2021 journal current protocols real time assessment of mitochondrial toxicity in hepg2 cells using the seahorse extracellular flux analyzer amos espinosa grace pohan michelle arkin sarine markossian doi https doi org 10 1021 acs jcim 0c00950 date january 27 2021 journal journal of chemical information and modeling machine learning models to predict inhibitors of the bile salt export pump kevin s mcloughlin claire g jeong thomas d sweitzer amanda j minnich margaret j tse brian j bennion jonathan e allen stacie calad thomson thomas s rush and james m brase doi https doi org 10 1124 dmd 120 000202 date february 2021 journal drug metabolism disposition predicting volume of distribution in humans performance of in silico methods for large set of structurally diverse clinical compounds neha murad kishore k pasikanti benjamin d madej amanda minnich juliet m mccomas sabrinia crouch joseph w polli and andrew d weber doi https doi org 10 1002 cpch 90 date december 14 2020 journal current protocols in chemical biology multiparametric high content assays to measure cell health and oxidative damage as a model for drug induced liver injury grace pohan jether amos espinosa steven chen kenny k ang michelle r arkin sarine markossian doi https doi org 10 3389 fphar 2020 00770 date june 30 2020 journal frontiers in pharmacology translational pharmacology accelerating therapeutics for opportunities in medicine a paradigm shift in drug discovery izumi v hinkson benjamin madej and eric a stahlberg on behalf of the atom consortium doi https doi org 10 1021 acs jcim 9b01053 date april 3 2020 journal journal of chemical information and models ampl a data driven modeling pipeline for drug discovery amanda j minnich kevin mcloughlin margaret tse jason deng andrew weber neha murad benjamin d madej bharath ramsundar tom rush stacie calad thomson jim brase and jonathan e allen doi https doi org 10 1038 s41573 019 0050 3 date december 4 2019 journal nature reviews drug discovery rethinking drug design in the artificial intelligence era petra schneider w patrick walters alleyn t plowright norman sieroka jennifer listgarten robert a goodnow jr jasmin fisher johanna m jansen josé s duca thomas s rush matthias zentgraf john edward hill elizabeth krutoholow matthias kohler jeff blaney kimito funatsu chris luebkemann gisbert schneider artificial intelligence and pharmacometrics time to embrace capitalize and advance ayyappa chaturvedula stacie calad thomson chao liu mark sale nandu gattu navin goyal doi https doi org 10 1002 psp4 12418 date april 21 2019 journal cpt pharmacometrics systems pharmacology we need to get better medicines to patients faster this project aims to do that alan ashworth president of ucsf helen diller family comprehensive cancer center news events news releases news releases march 29 2021 atom consortium welcomes three doe national laboratories to accelerate drug discovery march 29 2021 bringing the experience and expertise from three additional doe national laboratories to atom s current partners reinforces atom as a valuable national resource to create powerful new capabilities for the cancer research community building collaborations and driving advances in translational research to develop treatments more quickly said eric stahlberg director of the biomedical informatics and data science group at fnl and co lead of the atom consortium read more march 29 2021 may 20 2020 excelra to provide lawrence livermore national laboratory with small molecule medicinal chemistry intelligence data to help develop drug design platform may 20 2020 excelra will give llnl a member of the atom consortium full access to gostar a vast repository of approximately 8 million small molecule discovery compounds and read more may 20 2020 april 8 2019 atom consortium combines forces with nvidia to accelerate ai in drug discovery april 8 2019 drug discovery is in the perfect position to take full advantage of ai with advancements in high throughout technologies ai algorithms and high performance computing said kimberly powell vp of healthcare at nvidia read more april 8 2019 october 27 2017 public private consortium aims to cut preclinical cancer drug discovery from six years to just one october 27 2017 lawrence livermore national laboratory frederick national laboratory for cancer research gsk and university of california san francisco will combine vast data stores supercomputing and scientific expertise to reinvent discovery process for cancer medicines read more october 27 2017 atom blog atom blog atom is combining forces with nci to release data and models for the public good to support modac s objectives atom has released its best model and datasets into modac s repository for public users to use the idea is for the user to re use the machine learning models with atom s open source atom modeling pipeline ampl software to evaluate small molecule compounds against selected targets for their drug discovery or chemical toxicology research read more michelle arkin ask the expert in an interview with lab manager in michelle arkin s ph d ask the expert interview with lab manager she describes how atom is using machine learning and artificial intelligence to bring together data from public databases and from pharmaceutical partners to perform multi parameter optimization on a drug target coupled with atom s pipeline ampl to do automated experiments read more learn more about atom through our newsletters read more about atom s science from our researchers along with our recent publications also we share updates about our new partners technical team members and presentations read more second annual atom summer training program empowers and equips students the program aimed to teach the students how to write code perform machine learning analyze models and understand assay development they built the models using the open source rulebender software and ampl atom modeling pipeline packages their models and the abundance of analyzed data advance atom s modeling and molecular design program read more meet our atom summer trainees meet our new student trainees read more poster session poster winner amanda paulson of frederick national laboratory for cancer research won her poster session for the informatics category at the us army nci spring research festival read more purdue datamine project evaluation of atom capabilities purdue is answering the call for data science expertise with the data mine a unique program that promotes learning from data and transforming it into important information to help solve real world problems the students living in a community setting partner on projects with established corporations read more sc21 meet six trailblazing women in hpc while they comprise about 51 of the general population women account for only about 17 of the hpc workforce1 those numbers are slowly improving thanks to the contributions of numerous female engineers scientists and researchers read more atom posters at the sixth computational approaches for cancer workshop 2020 cafcw20 learn more about what our atom colleagues are doing at atom through their posters read more listen to brian van essen s talk on covid 19 drug design an acm gordon bell special prize for hpc based covid 19 research finalist join lawrence livermore national laboratory llnl on youtube to hear brian van essen led by sam ade jacobs work on covid 19 drug design at supercomputing2020 read more atom training and mentorship opportunity support an ai knowledgeable future workforce this summer instead of working at a traditional hospital or store pharmacy internship five butler university doctor of pharmacy students delved into the world of data science and machine learning under the mentorship of experts from the atom consortium read more atom tech team spotlight jillian yong one of the projects i m involved with has a goal of optimizing preclinical safety predictions so we can incorporate predictive toxicology and computational modelling early in the drug discovery process read more atom tech team spotlight dr neha murad neha murad ph d is a biomathematician and a postdoctoral researcher at atom neha has a keen interest in the biomedical applications of mathematics and read more reducing failure and attrition in drug discovery through in vitro and in silico dili predictions one of our goals at atom is to optimize preclinical safety predictions in silico so we can incorporate predictive toxicology early in the drug discovery process read more atom tech team spotlight dr amanda minnich amanda minnich ph d atom data scientist is spearheading the atom data driven modeling ddm integrated project team and has led the development of our automated ddm pipeline read more atom is ready to launch year 2 r d plan as atom gears up to implement its year 2 goals jim brase m s atom co lead of technology addressed the delegates at the atom 1 year anniversary event read more year in review our key achievements at the atom 1 year anniversary event this past october over 60 delegates from atom member organizations convened at atom headquarters team leaders shared the major accomplishments read more stay informed with periodic updates from our leadership and technical teams subscribe news news articles may 3 2021 belinda akpa engineering inclusive solutions may 3 2021 akpa s systems pharmacology models help set atom apart from other ai driven drug discovery methods she will leverage ornl s high performance computing capabilities such as the summit supercomputer in her quest to get drugs to patients faster with a greater probability of success read more may 3 2021 april 5 2021 beating back the coronavirus requires a bigger arsenal april 5 2021 tackling a virus requires a multipronged approach in the big picture way of not only having an arsenal to respond with as the virus changes over time but also recognizing that trying to kill something that s not really alive is a very hard task says marti head of oak ridge national laboratory ornl who leads the molecular design project of the national virtual biotechnology laboratory nvbl read more april 5 2021 november 23 2020 model for covid 19 drug discovery a gordon bell finalist november 23 2020 a machine learning model developed by a team of lawrence livermore national laboratory llnl scientists to aid in covid 19 drug discovery efforts is a finalist for the gordon bell special prize for high performance computing based covid 19 research read more november 23 2020 march 31 2020 doe expands on role of covid 19 supercomputing consortium march 31 2020 after announcing the launch of the covid 19 high performance computing consortium on sunday the department of energy yesterday provided more details on its scope and operation in a briefing led by undersecretary of energy paul dabbar and attended by hpc leaders from national labs the joint public private effort will pool 16 systems which together offer read more march 31 2020 march 26 2020 lab researchers aid covid 19 response in antibody anti viral research march 26 2020 lawrence livermore national laboratory scientists are contributing to the global fight against covid 19 by combining artificial intelligence machine learning bioinformatics and supercomputing to help discover read more march 26 2020 october 21 2019 the atom consortium october 21 2019 drug discovery has always been a slow and laborious process by nature with researchers finding dead ends much more frequently than successful routes to the clinic read more october 21 2019 october 1 2019 artificial intelligence in drug discovery hope or hype october 1 2019 at the world s pharma and biotech companies artificial intelligence is increasingly critical to the drug discovery engine read more october 1 2019 september 30 2019 argonne national laboratory to join atom to transform drug discovery with artificial intelligence september 30 2019 argonne has announced its commitment to become the newest member of atom a public private partnership between national laboratories academic institutions and private industry read more september 30 2019 may 1 2019 pytorch adds new dev tools as it hits production scale may 1 2019 since its release just a few months ago pytorch 1 0 has been rapidly adopted as a powerful flexible deep learning platform that enables engineers and researchers to move quickly from research to production read more may 1 2019 april 9 2019 nvidia ceo ties ai driven medical advances to data driven leaps in every industry april 9 2019 radiology autonomous vehicles supercomputing the changes sweeping through all these fields are closely related just ask nvidia ceo jensen huang read more april 9 2019 april 8 2019 fnl founded consortium partners with tech firm to advance ai drug discovery april 8 2019 a frederick national laboratory for cancer research founded organization has announced plans to partner with a california based technology company to advance its artificial intelligence drug discovery program read more april 8 2019 april 8 2019 nvidia doubles down on medical ai april 8 2019 nvidia is collaborating with medical groups to push gpu powered ai tools into clinical settings including radiology and drug discovery read more april 8 2019 april 8 2019 nvidia spins up its gpus to accelerate ai driven medical diagnosis and drug discovery april 8 2019 nvidia corp reckons artificial intelligence has evolved to the point where it can be reliably used to help diagnose diseases and discover new drugs read more april 8 2019 january 15 2019 artificial intelligence in drug discovery 2018 year in review january 15 2019 the idea of using artificial intelligence ai to accelerate drug discovery process and boost a success rate of pharmaceutical research programs has inspired a surge of activity in this area over the last several years read more january 15 2019 august 16 2018 transforming drug discovery by accelerating the development of more effective therapies august 16 2018 the recently established accelerating therapeutics for opportunities in medicine atom consortium was conceived by john with a mission to accelerate the development of more effective therapies for patients read more august 16 2018 may 16 2018 innovations in oncology the cancer moonshot and beyond may 16 2018 since its launch in 2016 the cancer moonshot initiative has successfully united leading international scientists from industry and academia whose collaborative efforts have been key to the delivery of more effective tools for cancer diagnosis treatment and prevention read more may 16 2018 may 4 2018 sharing dark data inside the atom initiative may 4 2018 data sharing initiative atom of which glaxosmithkline is a member wants ...